The Welshman, who took command of the ochre leader's jersey on Wednesday, was third across the line in the first sprint of the day on Thursday's third stage, which eventuated in a five second buffer over the day's victor, Tom Jelte Slagter (Blanco) in the overall.
"This race is always the same, it always comes down to a few seconds and bonuses always come into it," Thomas said post-stage.
The intermediate sprint bonus also ensured Thomas retained the lead in the sprint classification.
The 26-year-old was certain that Sky would have the gauntlet thrown at them from their rivals, and it took the steadying influence of Bernhard Eisel at the front of the bunch to ensure that the breakaway of Will Clarke (Argos Shimano) and Simon Clarke (Orica GreenEdge) was never allowed more than three-and-a half minutes before the race came back together for a bunch sprint after the Stirling circuit.
"We were always in control, but we were definitely tested and a lot of guys were attacking us," explained Thomas.
"It just shows it's an important race to everyone and everyone wants to do well. But the boys were tremendous, really, and I can't thank them enough.
"It was down to me at the end to try and get a podium and a couple of bonus seconds. I didn't quite do that, but we still have the jersey and that's the main thing."
There was one nervous moment for the team when last year's third overall, Tiago Machado (RadioShack Leopard), attacked towards the end of the final lap but it was another of Thomas' teammates who was able to rise to the challenge.
"Hayman was super-strong and I trusted him to bring it back - it was perfect," he said.
With Friday’s stage to Tanunda set to be one for the sprinters, the GC is not likely to be affected unduly, meaning that regardless of the placement of Corkscrew Hill early in the week, the race will be decided on Saturday at Willunga, ahead of the traditional final criterium in Adelaide.